After he was located and questioned, he was released and removed from the FBI's wanted list.
Khan's father, Agha Abdul Khan, owned a pharmaceutical firm. Khan graduated from the medical school at Aga Khan University in Karachi in 1995.
When Aafia Siddiqui met his mother in Pakistan, his parents agreed on an arranged marriage for him and met with Siddiqui's parents to discuss the details. It was decided that since Siddiqui had been accepted into Brandeis University in Boston, Khan could move to Lexington, Massachusetts, with her and begin studies at Harvard University. Since Siddiqui was back in the United States, the couple, who had never seen each other, performed their nikah over the telephone in 1995. He has also said that Siddiqui wanted him to move to Afghanistan, and work as a medic for the mujahideen. They have three children: Ahmed (b. 1996), Maryam (b. 1998), and Suleman (b. 2002). The two older children are American citizens.
After approximately a year in Lexington, the couple moved to Back Bay Manor, in Mission Hill to be closer to Khan's hospital. In 1999, while living in Boston, Siddiqui and her husband founded the nonprofit Institute of Islamic Research and Teaching. They moved again in July 2001, this time to Malden. Their lease was taken over by Saudi nationals Abdullah Al Reshood and Hatem Al Dhahri, who had just received a $20,000 transfer from the Saudi government, ostensibly to pay for medical treatment for al-Reshood's wife.
Siddiqui's family claim that Khan was an abusive husband, and her colleagues at university reported that she often came in with bruises on her face. Khan admits that on one occasion, he threw a baby bottle at her face, splitting her lip, requiring stitches in the hospital.
According to Khan, after the September 11 attacks Siddiqui insisted on leaving the U.S., saying that it was unsafe for them and their children to remain because the U.S. government was abducting Muslim children. She had previously spoken of wanting to immigrate to Afghanistan or Bosnia. Khan balked, fearful he would lose his salary bonus at the hospital, and agreed she could go ahead and he would follow shortly. However, others dispute that the move was his idea, and suggest that Khan had been "more fundamentalist in his religious beliefs than her", and she wanted to remain in the United States while he had insisted on raising their children in an Islamic country.
Khan returned to the United States with his family on January 5, 2002, claiming he had been unable to find suitable employment in Pakistan.
In May 2002, the FBI questioned the couple regarding their purchase over the internet of $10,000 worth of night vision goggles, body armor, and military manuals, including The Anarchist's Arsenal, Fugitive, Advanced Fugitive, and How to Make C-4. Khan claimed that these were for hunting and camping expeditions.
His mother-in-law claims that he was responsible for the investigation into Siddiqui, purchasing the suspicious items using her e-mail account, to be shipped to Pakistan shortly before they moved there.
In addition, the couple had transferred $8,000 to their Pakistani account with Habib Bank on December 21. Khan agreed to return the items he had purchased.
On June 26, 2002, the couple returned to Pakistan. They said it was to be with Siddiqui's father, who was ill.
In Pakistan, their families said there was visible tension between the couple, with Khan telling a relative that "her nature doesn't suit me". He has accused Siddiqui of being abusive and manipulative throughout their seven years of marriage, and said that Siddiqui had a violent personality and extremist views, leading him to suspect her of involvement in jihadi activities.
In August 2002 the couple's marriage reached a breaking point. Around this time, Khan went to the bank to withdraw $2,000 only to be told that his wife had already removed the money from the account earlier, leading to a heated argument. Angered, Khan went to Siddiqui's parents' home, and said he intended to divorce her. An argument took place between Khan and her father, and Siddiqui's father suffered a fatal heart attack on August 15, 2002. Her family refused all future contact with Khan. A few weeks later Siddiqui gave birth to their third child. Their divorce was finalized on October 21, 2002.
Khan claims he helped the ISI identify his ex-wife, whom they arrested as she returned to Jinnah International Airport from an overseas trip. She was questioned by the FBI, and American intelligence sources confirmed that she was "essentially in the hands of the FBI now". Siddiqui's family claimed that Khan was responsible for her "disappearance" that month. For his role, Siddiqui's family launched a PKR5 million lawsuit alleging he is an "Islamic extremist" "wifebeater" who defamed his ex-wife and lies about her militant connections.
Within weeks, he was added to the FBI Seeking Information - War on Terrorism list. He was eventually removed from the list.
As of 2005, he practiced medicine in Karachi.
Siddiqui was accused of being an al-Qaeda member. In February 2010, she was convicted of assault with a deadly weapon and attempting to kill U.S. soldiers and FBI agents who were seeking to interrogate her while she was in custody.